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- PDB-4ldc: Crystal Structure of DOC2B C2B domain -

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Basic information

Entry
Database: PDB / ID: 4ldc
TitleCrystal Structure of DOC2B C2B domain
ComponentsDouble C2-like domain-containing protein beta
KeywordsMETAL BINDING PROTEIN / C2 / Calcium binding domain
Function / homology
Function and homology information


calcium-dependent activation of synaptic vesicle fusion / spontaneous neurotransmitter secretion / positive regulation of vesicle fusion / extrinsic component of synaptic vesicle membrane / calcium ion-regulated exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis / regulation of calcium ion-dependent exocytosis / calcium-dependent phospholipid binding / syntaxin binding / exocytosis ...calcium-dependent activation of synaptic vesicle fusion / spontaneous neurotransmitter secretion / positive regulation of vesicle fusion / extrinsic component of synaptic vesicle membrane / calcium ion-regulated exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis / regulation of calcium ion-dependent exocytosis / calcium-dependent phospholipid binding / syntaxin binding / exocytosis / protein localization / positive regulation of insulin secretion / glutamatergic synapse / synapse / calcium ion binding / plasma membrane / cytoplasm
Similarity search - Function
Double C2 protein, alpha/beta/gamma / : / Rabphilin/DOC2/Noc2 / Synaptotagmin / C2 domain / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily ...Double C2 protein, alpha/beta/gamma / : / Rabphilin/DOC2/Noc2 / Synaptotagmin / C2 domain / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CITRATE ANION / Double C2-like domain-containing protein beta
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.264 Å
AuthorsGiladi, M. / Almagor, L. / Hirsch, J.A.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: The C2B Domain Is the Primary Ca(2+) Sensor in DOC2B: A Structural and Functional Analysis.
Authors: Giladi, M. / Michaeli, L. / Almagor, L. / Bar-On, D. / Buki, T. / Ashery, U. / Khananshvili, D. / Hirsch, J.A.
History
DepositionJun 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Double C2-like domain-containing protein beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2374
Polymers16,9681
Non-polymers2693
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.802, 40.091, 36.922
Angle α, β, γ (deg.)90.00, 105.47, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-649-

HOH

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Components

#1: Protein Double C2-like domain-containing protein beta / Doc2-beta


Mass: 16967.500 Da / Num. of mol.: 1 / Fragment: C2B domain (UNP residues 265-412)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Doc2b / Production host: Escherichia coli (E. coli) / References: UniProt: P70610
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.56 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: 22.5% isopropanol, 20% PEG 4000, 0.1 M Na-citrate, pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 28, 2012
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.24→50 Å / Num. all: 33561 / Num. obs: 33561 / % possible obs: 92.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 1.24→1.28 Å / % possible all: 29.4

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIX(phenix.refine: 1.8_1069)model building
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8_1069phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.264→36.448 Å / SU ML: 0.09 / σ(F): 1.34 / Phase error: 13.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1442 1683 5.02 %RANDOM
Rwork0.1269 ---
obs0.1278 33558 97.7 %-
all-33561 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.264→36.448 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1163 0 15 214 1392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111243
X-RAY DIFFRACTIONf_angle_d1.1061702
X-RAY DIFFRACTIONf_dihedral_angle_d12.196469
X-RAY DIFFRACTIONf_chiral_restr0.065182
X-RAY DIFFRACTIONf_plane_restr0.005215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.264-1.30150.16641370.12862569X-RAY DIFFRACTION96
1.3015-1.34350.15821380.10982653X-RAY DIFFRACTION98
1.3435-1.39150.15741410.10972662X-RAY DIFFRACTION99
1.3915-1.44720.15511390.11312681X-RAY DIFFRACTION99
1.4472-1.51310.16161440.11262697X-RAY DIFFRACTION99
1.5131-1.59290.14011400.10832683X-RAY DIFFRACTION99
1.5929-1.69270.14421430.10782679X-RAY DIFFRACTION99
1.6927-1.82340.12461440.11282685X-RAY DIFFRACTION99
1.8234-2.00680.13461400.11352678X-RAY DIFFRACTION99
2.0068-2.29720.14731420.11892660X-RAY DIFFRACTION98
2.2972-2.8940.13961390.13822638X-RAY DIFFRACTION96
2.894-36.46340.1441360.1582590X-RAY DIFFRACTION92

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